cmap: CMap2 LFC Signature Database

In yduan004/signatureSearchData: Datasets for signatureSearch package

CMap2 LFC Signature Database

Description

The MAS5 normalized CEL files from the help file of cmap_expr can be used for differential expression (DE) analysis with 'limma' package to get a matrix containing the LFC (log2 fold change) scores. The columns of the matrix are the treatment v.s. control instances, which is defined in the 'cmap_instances_02.txt' file downloaded from CMap project website. The same as the 'cmap_rank' database, only one treatment condition is selected for a compound in a cell. The resulting matrix represents LFC of 12,403 genes for 1,281 compound treatments in up to 5 cells (3,478 signatures in total). The latter was stored in an HDF5 file, which is referred to as the cmap database. Note, The number of compound treatments in cmap database is slightly different from that of the cmap_expr database. The reason is that some of the compound treatment is discarded if the number of control and treatment samples are less than 3 during the DE analysis.

Details

The cmap database can be downloaded as HDF5 file from Bioconductor’s ExperimentHub as shown in the Example section.

The same as the cmap_expr dataset, the loaded cmap data object is also generated from the raw CEL files downloaded from the CMap project site and processed as describe above.

Examples

library(ExperimentHub)
# eh <- ExperimentHub()
# query(eh, c("signatureSearchData", "cmap"))
# cmap_path <- eh[["EH3223"]]
# rhdf5::h5ls(cmap_path)

yduan004/signatureSearchData documentation built on April 7, 2023, 4:12 a.m.